http://creativecommons.org/licenses/by-sa/2.0/

1
http//creativecommons.org/licenses/by-sa/2.0/
2
An Introduction to Perl for Bioinformatics Part
1

• Will Hsiao
• Simon Fraser University
• Department of Molecular Biology and Biochemistry
• wwhsiao_at_sfu.ca
• www.pathogenomics.sfu.ca/brinkman

3
Outline

• Session 1
• Review of the previous day
• Perl historical perspective
• Expand on Regular Expression
• General Use of Perl
• Expand on Perl Functions and introduce Modules
• Interactive demo on Modules
• Break
• Session 2
• Use of Perl in Bioinformatics
• Object Oriented Perl
• Bioperl Overview
• Interactive demo on Bioperl
• Introduction to the Perl assignment

4
Todays Goals

• Will have become familiar with a few more
  advanced programming concepts
• Regular Expression
• Functions and Modules
• Object Oriented Perl
• Will have heard a few common uses of Perl
• Will have learned how Perl can be used in
  bioinformatics
• Will have discovered Bioperl

5
Recap from Yesterday

• Which ones below are variables?
• sequence, _at_sequences, 74, I knew this,
  seq_id, exciting stuff
• What are functions?
• Which part of the statement below is a function
• _at_sequences split (/\t/, genome)
• Other issues?

6
What does this program do?

• !/usr/bin/perl w
• a mystery subroutine that does something
• sub mystery_function
• my (seq1, seq2)_at__
• my rDNA reverse seq1
• seq2 tr/T/U/
• my hybrid rDNA.seq2
• return hybrid
• body of the main program
• DNA1 GATACAATAC
• DNA2 ATCGTAATCC
• answer mystery_function(DNA1, DNA2)
• print answer\n

7
use strict

• !/usr/bin/perl w
• use strict
• a mystery subroutine that does something
• sub mystery_function
• my (seq1, seq2)_at__
• my rDNA reverse seq1
• seq2 tr/T/U/
• my hybrid rDNA.seq2
• return hybrid
• body of the main program
• my DNA1 GATACAATAC
• my DNA2 ATCGTAATCC
• my answer mystery_function(DNA1, DNA2)
• print answer\n

8
Effects of use strict

• Requires you to declare variables
• Warns you about possible typos in variables

9
Why bother use strict

• Enforces some good programming rules
• Helps to prevent silly errors
• Makes trouble shooting your program easier
• Becomes essential as your code becomes longer
• We will use strict in all the code you see today
  and in your assignment
• Bottom line ALWAYS use strict

10
Perl a brief history

• Purpose for scanning arbitrary text files,
  extracting information from those text files, and
  printing reports based on that information
• - from perl manpage
• 1987-Perl 1.0 released
• 1993 CPAN conceived
• 1995 Perl 5.000 released
• Object oriented perl
• Modules for creating interactive web pages (CGI)
• Modules for connection to databases (DBI)
• Current stable version of Perl is 5.8.5

11
How do we manipulate text?
Regular Expression
12
What is Regular Expression

• REGEX provides pattern matching ability
• Tells you whether a string contains a pattern or
  not (Note its a yes or no question!)

I have a golden retriever
Yesterday I saw a big black dog
Dog! Humans best friend
Regular Expression looking for dog
No or False
No b/c REGEX is case sensitive
Yes or True
Yes or True
13
Why need Regular Expression

• Human does this quite well
• But.
• Imagine trying to find all ATGs in the human
  genome by hand
• Furthermore, imagine trying to find all EcoRI
  digestion sites (GAATTC) in the human genome

14
Perl REGEX example

• my text Bioinformatics Kicks Ass
• if (text/Kicks/)
• print The text contains Kicks\n

• is the binding operator
• It says does the string on the left contain the
  pattern on the right?
• /Kicks/ is my pattern
• The matching operation results in a true or false
  answer

15
More Regular Expression

• A pattern that match only one string is not very
  useful!
• We need symbols to represent classes of strings
• REGEX is its own little language inside Perl
• Has different syntax and symbols!
• Symbols which you have used in perl such as .
  have totally different meanings in REGEX

16
REGEX Metacharacters

• Metacharacters allow a pattern to match different
  strings
• Wildcards are examples of metacharacters
• /.ick/ will match kick, sick, tick,
  stick, kicks, etc.
• Perl REGEX has much more powerful metacharacters
  used to represent classes of characters

17
Types of Metacharacters

• . matches any one character or space except \n
• denotes a selection of characters and matches
  ONE of the characters in the selection.
• What does ATCG match?
• \t, \s, \n match a tab, a space and a newline
  respectively
• \w matches any characters in a-zA-Z0-9
• \d matches 0-9
• \D matches anything except 0-9

18
An Example of Metacharacters

• V1S 5A6?
• /\w\d\D\s\d.0-9/
• Is it a good pattern for postal code?
• What else does it match?

19
REGEX Quantifiers

• What if you want to match a character more than
  once?
• What if you want to match an mRNA with a polyA
  tail that is at least 5 12 As?
• ATGAAAAAAAAAAA

20
REGEX Quantifiers
ATGAAAAAAAAAAA
/ATGATCGA5,12/

• matches one or more copies of the previous
  character
• matches zero or more copies of the previous
  character
• ? matches zero or one copy of the previous
  character
• min,max matches a number of copies within the
  specified range

21
REGEX Anchors

• The previous pattern is not strictly correct
  because
• Itll match a string that doesnt start with ATG
• Itll match a string that doesnt end with poly
  As
• Anchors tell REGEX that a pattern must occur at
  the beginning or at the end of a string

22
REGEX Anchors

• anchors the pattern to the start of a string
• anchors the pattern to the end of a string
• /ATGATCGA5,12/

23
REGEX is greedy!

• The revised pattern is still incorrect because
• Itll match a string that has more than 12 As at
  the end
• quantifiers will try to match as many copies of a
  sub-pattern as possible!
• /ATGATCGA5,12/
• ATGGCCCGGCCTTTCCCAAAAAAAAAAAA
• ATGGCCCGGCCTTTCCCAAAAAAAAAAAA

24
Curb that Greed!

• ? after a quantifier prevensts REGEX from being
  greed
• note this is the second use of the question mark
• What is the other use of ? in REGEX?
• /ATGATCG?A5,12/
• ATGGCCCGGCCTTTCCGAAAAAAAAAAAA
• ATGGCCCGGCCTTTCCGAAAAAAAAAAAA

25
REGEX Capture

• What if you want to keep the part of a string
  that matches to your pattern?
• Use ( ) memory parentheses

ATGGCCCGGCCTTTCCGAAAAAAAAAAAA
/ATG(ATCG?)A5,12/
26
REGEX Capture
/ATG(ATCG?)(A5,12)/
1
2

• Whats inside the first ( ) is assigned to 1
• Whats inside the Second ( ) is 2 and so on
• So 2 eq AAAAAAAAAAAA

27
REGEX Modifiers

• Modifiers come after a pattern and affect the
  entire pattern
• You have seen //g already which does global
  matching (/T/g) and global replacement(s/T/U/g)
• Other useful modifiers

28
REGEX Demo

• Demonstrate quantifiers
• Demonstrate anchors
• Demonstrate //i
• Demonstrate capture
• Demonstrate the effect of greedy vs. non-greedy
• Demonstrate metacharacters

29
Other binding operators

• is called the binding operator which binds
  the a string on the left to a pattern on the
  right
• E.g. text /PATTERN/
• Two other binding operators s/// and tr///
• s/// (substitution) substitutes a matched
  pattern by a string (kind of like the replace
  function in MS Word)
• tr/// (translation) translates a character to
  another

30
Summary on REGEX

• REGEX is its own little language!!!
• REGEX is used in some functions (e.g. split)
• Perl REGEX extremely powerful and fast
• REGEX is one of the main strengths of Perl
• To learn more
• Learning Perl (3rd ed.) Chapters 7, 8, 9
• Programming Perl (3rd ed.) Chapter 5
• Mastering Regular Expression (2nd ed.)

31
Common Uses of Perl

• REGEX
• Complete set of tools for pattern matching text
• System administration
• Perl scripts can be written to automate many
  system administration tasks
• CGI.pm
• Module for designing interactive web pages
• DBI.pm
• Database Interface allows communication between
  all major RDBMS systems (Oracle, MySQL, etc.)

32
Review on Functions

• How do we call a function?
• my sum add (2, 3)
• Functions can take some input values (parameters)
  and can return some output values
• You need to assign the return values to a
  variable in order to use them

33
More Review on Functions

• Benefits of subroutines
• Decompose a big problem into smaller, more
  manageable problems
• Organize your code
• Improve code reuse
• Easier to test and debug your code

sub add some code that adds numbers
here return the sum
34
What are Modules

• a logical collection of functions
• Each collection (or module) has its own name
  space
• Name space a table containing the names of
  variables and functions used in your code

35
Why is name space important
Package SEQanalysis_DNA
Package SEQanalysis_Prot
DNA ATGAATACTACTAT polyAtail
AAAAAAAAAA sub Revcom reverse complement
sequence sub concat concatenate two DNA
sequences
exon1 MEDAVRSKNTMI exon2
RSVADEGFLSMIRQH sub findmotif find a
peptide motif sub concat concatenate two exon
sequences
SEQanalysis_DNAconcat
SEQanalysis_Protconcat
36
Why Use Modules

• Modules allow you to use others code to extend
  the functionality of your program
• But, use other peoples modules is like going to
  other peoples houses
• Not everything will be the way you like it
• Read the module documentation
• Be nice
• use a module as it is intended
• In Perl, each module is a file stored in some
  directory in your system
• E.g. you can find cgi.pm in /usr/lib/ on your
  system (ask Graeme where it is)

37
Use Modules

• To use a module
• use ltmodulenamegt
• Examples
• use strict
• use Env
• use cgi qw(standard)
• To find out where modules are installed perl V
  
• To find out what standard modules are available
  perldoc perlmodlib

38
Module Demo

• Demonstrate perldoc as a method to read module
  documentation
• Demonstrate the difference before and after using
  a module (use strict and use Env)
• Demonstrate the perl V and an example of
  directory structure of modules

39
Where to find modules

• CPAN Comprehensive Perl Archive Network
• Central repository for Perl modules and more
• If its written in Perl, and its helpful and
  free, its probably on CPAN
• http//www.perl.com/CPAN/
• To install modules from CPAN
• perl MCPAN e install SomeModule
• Module dependency is taken cared of automatically
• Youll (usually) need to be root to install a
  module successfully
• For details see your notes

40
CPAN Web Demo

• Demonstrate how to search for a module and how to
  access the online documentation
• Well use GetoptLong as an example

41
Interactive Demo on GetoptLong

• Open your laptop!
• Open a terminal window
• Type cd /perl_two
• Type emacs ./getopt_demo.pl
• Lets go over the example together

42
Summary for Session 1

• Always use strict
• Regular Expression is its own language inside
  Perl
• I encourage you to read the chapters on REGEX in
  Learning Perl
• A module is a logical collection of functions
• You can find module documentation by using
  perldoc (command line) or by going online to CPAN

43
Break